UC Santa Barbara

The global climate is in crisis, and change through disruptive technological innovation is the only option for humanity to avoid catastrophic collapses of ecosystems, economies, and, ultimately, the ability of our planet to support human life on its current magnitude. Replacing unsustainable industrial practices with novel and green processes is one area of technology that could help mitigate petroleum dependence and, by extension, damage to the biosphere. Biorefineries use synthetic biology to achieve chemical production from renewable feedstocks. Of these, lignocellulosic biorefineries that convert plant cell walls into valuable chemicals are one especially attractive concept, as lignocellulose is the most abundant renewable carbon pool in the biosphere. A central technical challenge of the lignocellulosic biorefinery concept is depolymerizing recalcitrant polymers so they can be upgraded using complementary biological and abiotic processes. Lignin is the most recalcitrant faction of plant cell walls, and this polymer is chemically distinct from the polysaccharides it protects. The aromaticity of lignin presents both a challenge and opportunity since this chemistry imparts essential properties to plant cell walls, such as hydrophobicity and resistance to degradation, that are also desirable in important consumer products like plastics. Innovation in lignin deconstruction is a current focus of lignocellulosic biorefinery research, and novel ways to degrade this polymer that are inspired by biology could help address this challenge. Large herbivores and their microbial gut communities convert lignocellulose into other chemicals at a rate and yield that eclipses our current best lignocellulosic biorefineries. My work seeks to discover the unknown aspects of biological lignin degradation as it occurs in herbivore gut microbiomes by focusing on a group of highly specialized lignocellulose degraders, The anaerobic gut fungi or Neocallimastigomycetes are some of the most proficient lignocellulose degraders documented to date, and in my work, I interrogate interactions between these organisms and lignin. The work is designed to increase understanding of how Neocallimastigomycetes depolymerize and eventually use carbon in lignin. During this pursuit, I have participated in every aspect of investigating these unique organisms, from enrichment and isolation to the heterologous expression of Neocallimastigomycete proteins in model organisms. My approach has been to match measurements of biochemistry and polymer chemistry, such as nuclear magnetic resonance, to measurements of biological activity. Along the way, I leveraged my extensive experience in biochemistry and metabolism to increase knowledge pertaining to the basic biology of the Neocallimastigomycetes. The most notable finding I present in this thesis is the discovery that anaerobic fungi from class Neocallimastigomycetes can deconstruct lignin, and this is the first instance in which anyone has measured this bond scission by an anaerobic microbe. Surrounding this finding, I also present advances in understanding syntrophic relationships between bacteria, fungi, and archaea and novel aspects of the responsive metabolism of Neocallimastigomycete fungi. The presented findings increase understanding of herbivore digestion, anaerobic microbiology, and refinement of lignocellulose into value-added chemicals. Many of my publications raise more questions than they answer, but this is the nature of creating new knowledge. Despite the new questions raised and extensive progress still required for biotechnology to help mitigate the climate crisis, the work in this dissertation is a small step forward in creating sustainable biotechnology inspired by nature.